Contacts of the helix formed by residues 335 - 346 (chain C) in PDB entry 5LK5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 335 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 3.6 26.1 - - + +
92C VAL* 4.1 3.1 - - - -
333C THR* 3.5 13.0 + - - +
334C ASN* 1.3 86.7 - - - +
336C GLU* 1.3 58.8 + - - +
337C ALA* 3.0 23.1 + - - +
338C TYR* 3.1 21.2 + - + +
339C ALA* 3.0 23.2 + - - +
356F GLN* 4.5 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 4.2 13.7 + - + +
92C VAL* 4.0 7.9 - - - +
175C ILE* 3.7 31.5 - - + +
177C ARG* 2.7 47.0 + - - +
183C GLU* 4.4 3.3 - - - +
185C LYS* 5.2 9.5 + - - +
334C ASN 4.2 0.6 + - - -
335C ASP* 1.3 69.9 + - - +
337C ALA* 1.3 64.7 + - - +
339C ALA* 3.4 6.0 + - - +
340C GLU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ASP* 3.0 7.7 + - - +
336C GLU* 1.3 78.6 - - - +
338C TYR* 1.3 62.9 + - - +
340C GLU* 3.1 5.2 + - - +
341C GLU* 3.0 31.3 + - - +
352F ALA* 4.3 23.6 - - + +
353F ALA* 4.5 9.6 - - + +
356F GLN* 3.2 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 4.7 12.1 - - + -
21C VAL* 4.0 22.4 - - + +
24C LYS* 2.6 27.5 + - - -
331C LEU* 4.1 21.3 - - + -
333C THR* 4.0 15.5 - - - -
335C ASP* 3.1 27.9 + - + +
336C GLU 3.3 0.2 - - - -
337C ALA* 1.3 75.8 - - - +
339C ALA* 1.3 67.8 + - - +
341C GLU* 3.2 27.3 + - + +
342C PHE* 2.9 32.4 + - + +
345C GLU* 5.3 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C VAL* 3.7 30.3 - - + -
94C GLN* 2.9 35.1 + - - +
173C THR* 4.9 2.9 - - + -
175C ILE* 5.5 0.7 - - + -
331C LEU* 3.8 15.7 - - + -
333C THR* 4.1 5.1 - - + +
335C ASP 3.0 11.7 + - - +
336C GLU* 3.5 9.6 - - - +
338C TYR* 1.3 77.6 - - - +
340C GLU* 1.3 57.0 + - - +
342C PHE* 3.5 0.3 + - - +
343C GLY* 3.0 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 5.1 0.2 - - - -
185C LYS* 3.7 19.9 + - - +
188C ASN* 3.0 41.5 + - - +
336C GLU 3.1 13.2 + - - +
337C ALA* 3.1 9.5 + - - +
339C ALA* 1.3 74.6 - - - +
341C GLU* 1.3 65.1 + - - +
343C GLY 3.3 0.2 + - - -
344C ASN* 3.0 27.9 + - - +
348F GLY 5.4 1.3 - - - +
351F LYS* 2.8 37.2 + - - +
352F ALA* 3.6 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ALA* 3.0 25.3 + - - +
338C TYR* 3.4 28.7 - - + +
340C GLU* 1.3 76.3 - - + +
342C PHE* 1.3 63.4 + - - +
344C ASN* 3.1 4.7 + - - +
345C GLU* 3.0 33.0 + - - +
62F LYS* 5.9 0.5 + - - -
348F GLY 4.6 9.4 - - - +
349F VAL* 3.7 34.2 - - + +
352F ALA* 5.6 4.9 - - + +
353F ALA* 3.8 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LYS* 3.5 36.6 - - + -
26C GLN* 3.6 34.5 - - + -
94C GLN* 4.1 7.4 - - - -
329C ASN* 3.9 15.9 - - + -
330C PHE 4.1 3.4 - - - -
331C LEU* 3.7 38.6 - - + -
338C TYR* 2.9 25.8 + - + +
339C ALA 3.8 3.4 - - - +
341C GLU* 1.3 77.0 - - - +
343C GLY* 1.3 52.4 + - - +
345C GLU* 3.3 16.1 + - + -
346C THR* 2.7 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 3.6 15.2 - - - +
171C LEU* 3.7 18.4 - - - -
188C ASN* 3.9 5.6 - - - -
339C ALA 3.0 11.4 + - - -
340C GLU 3.7 4.3 - - - -
341C GLU 3.2 0.4 - - - -
342C PHE* 1.3 74.6 - - - +
344C ASN* 1.3 59.0 + - - +
346C THR* 3.6 5.2 - - - -
347C TRP* 3.1 15.2 + - - +
348C GLY 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ASN* 2.9 21.6 + - - +
340C GLU* 3.0 23.2 + - - +
341C GLU 3.1 7.2 + - - +
343C GLY* 1.3 77.6 - - - +
345C GLU* 1.3 57.8 + - - +
346C THR 3.3 0.2 - - - -
347C TRP* 4.0 13.5 - - - -
348C GLY* 3.4 22.9 - - - -
349C VAL* 3.5 6.1 + - - +
344F ASN* 3.6 36.1 - - + +
347F TRP* 5.7 1.8 - - - -
348F GLY* 2.8 32.3 + - - +
349F VAL* 5.1 0.2 - - + -
351F LYS* 5.0 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C TYR* 5.3 5.5 + - - -
341C GLU* 3.0 24.2 + - - +
342C PHE* 3.3 20.8 + - + +
344C ASN* 1.3 75.8 - - - +
346C THR* 1.3 63.7 + - + +
349C VAL* 3.4 22.5 - - - +
62F LYS* 4.8 6.6 + - - -
345F GLU* 5.0 9.2 - - + -
349F VAL* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 3.7 17.0 - - - +
96C THR* 4.9 0.2 - - - +
171C LEU* 4.7 4.0 - - - +
329C ASN* 3.4 40.3 - - - +
342C PHE* 2.7 40.2 + - + +
343C GLY* 3.3 7.1 + - - -
345C GLU* 1.3 82.1 - - + +
347C TRP* 1.3 73.2 + - - +
348C GLY 3.1 0.4 - - - -
349C VAL* 3.0 13.9 + - - +
350C THR* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il